Gene/Protein Disease Symptom Drug Enzyme Compound
Pivot Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound   Target Concepts: Gene/Protein Disease Symptom Drug Enzyme Compound

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Query: EC:2.7.7.6 (RNA polymerase)
34,946 document(s) hit in 31,850,051 MEDLINE articles (0.00 seconds)

The control of gene expression during development, differentiation and maintenance of cellular function is governed by a complex array of transcription factors. We have undertaken a molecular dissection of the regulatory factors that direct transcription of protein coding genes by RNA polymerase II. Our early studies identified sequence-specific transcriptional activators that bind to enhancer and promoter sequences to modulate the transcriptional initiation event. However, the mechanism by which activators enhance transcription and mediate promoter selectivity remained unknown. Combining biochemical purification and in vitro assays, we have recently identified an essential class of transcription factors called TAFs that are tightly associated with the basal factor TBP (TATA-binding protein). We have found that TAFs are responsible for at least two regulatory functions. Some TAFs serve as coactivators capable of binding activators and mediating enhancing function. Other TAFs have been shown to confer template selectivity by binding directly to core DNA elements of the promoter. Thus different subunits of TBP/TAF complexes perform a variety of functions critical for transcriptional regulation in animal cells.
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PMID:The biochemistry of transcription in eukaryotes: a paradigm for multisubunit regulatory complexes. 873 71

The binding of TBP (TFIID) to the TATA box has been considered to direct promoter recognition and pre-initiation complex formation because it is the first event leading to basal transcription by RNA polymerase II. Here, we analyse the binding of yeast TBP to a consensus TATAAA box and two point mutations, TAAAAA (inactive) and TATATA (active). Despite the fact that the TAAAAA sequence does not support transcription in vitro, yeast TBP binds the three sequences showing, in this sense, only a limited sequence specificity. However, the TBP-TAAAAA complex cannot be recognised by other basal transcription factors, in particular by TFIIB. DNase I footprinting patterns of the TBP-TAAAAA complex are different from those observed in functional TBP-TATA box complexes, indicating that, most likely, it is a different spatial arrangement of the TBP-DNA complex that prevents formation of the TFIIB-TBP-TAAAAA complex, also seriously impairing entry of TFIIA to the complex. DNA deformability of the A/T-rich sequences appears to be an important determinant in the formation of a productive TBP-TATA complex. These results indicate that the transcriptional competence of A/T-rich sequences is determined not only by TBP binding, but also by the ability of other basal transcription factors to recognise the preformed TBP-DNA complexes.
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PMID:TBP binds the transcriptionally inactive TA5 sequence but the resulting complex is not efficiently recognised by TFIIB and TFIIA. 876 Aug 79

Four new studies of the assembly of different subsets of the preinitiation complex of RNA polymerase II have provided insight into how transcription factors interact with each other and with DNA. A heterotetramer of TBP-associated factors shows a histone-like fold.
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PMID:Pieces of the puzzle: assembling the preinitiation complex of Pol II. 880 73

The core promoters for mammalian protein-coding genes often contain a TATA box, an initiator (Inr) element, or both of these control elements. The TFIID complex is essential both for TATA activity and for the activity of a common class of Inr elements characterized by an approximate consensus sequence PyPyA+1NT/APyPy. Although the complete set of proteins required for basal TATA-mediated transcription has been established, the requirements for TFIID-dependent Inr activity remain undefined. In this study we set out to reconstitute Inr activity with purified and recombinant general transcription factors. For this analysis, Inr activity was measured as the ability of an Inr to enhance the strength of a core promoter containing an upstream TATA box. Inr activity was not detected in reactions containing TFIIB, RAP30, RAP74, RNA polymerase II, and either TBP or TFIID, even though these factors were sufficient for TATA-mediated transcription from supercoiled templates. By use of a complementation assay, a factor that imparts Inr activity was identified. This factor, named CIF, stimulated Inr activity in reactions containing the TFIID complex, but activity was not detected with TBP. Further characterization of CIF suggested that it contains multiple components. Functional and immunological experiments demonstrated that one of the CIF components is the mammalian homolog of Drosophila TAF(II)150, which is not tightly associated with mammalian TFIID. These results reveal significant differences in the factor requirements for basal TATA and Inr activity. Further elucidation of these differences is likely to explain the need for the core promoter heterogeneity found within protein-coding genes.
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PMID:CIF, an essential cofactor for TFIID-dependent initiator function. 884 23

Transcription of tRNA genes by RNA polymerase III is controlled by the internal conserved sequences within the coding region and the immediate upstream flanking sequences. A highly transcribed copy of glycyl tRNA gene tRNA1Gly-1 from Bombyx mori is down regulated by sequences located much farther upstream in the region -150 to -300 nucleotides (nt), with respect to the +1 nt of tRNA. The negative regulatory effect has been narrowed down to a sequence motif 'TATATAA', a perfect consensus recognised by the TATA binding protein, TBP. This sequence element, when brought closer to the transcription start point, on the other hand, exerts a positive effect by promoting transcription of the gene devoid of other cis regulatory elements. The identity of the nuclear protein interacting with this 'TATATAA' element to TBP has been established by antibody and mutagenesis studies. The 'TATATAA' element thus influences the transcription of tRNA genes positively or negatively in a position-dependent manner either by recruitment or sequestration of TBP from the transcription machinery.
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PMID:Role of TATATAA element in the regulation of tRNA1Gly gene expression in Bombyx mori is position dependent. 889 51

Nonhistone proteins 6A and 6B (NHP6A/B) are nonsequence-specific DNA-binding proteins from Saccharomyces cerevisiae that are related structurally and functionally to the mammalian high mobility group proteins 1 and 2. These DNA architectural proteins distort DNA structure severely and have been shown to promote assembly of specialized recombination complexes. Here we show that the yeast NHP6A/B proteins are required for the induction of a subset of genes transcribed by RNA polymerase II (pol II). Activation of the CUP1, CYC1, GAL1, and DDR2 genes was decreased or abolished completely in the delta nhp6A/B strain. No significant change in basal expression was observed for any of the 10 genes examined. Analysis of chimeric gene constructs localized the regions dependent on NHP6A/B to be primarily at the core promoters, although the GAL1 UAS also requires NHP6A/B for activity. In vitro, NHP6A stimulated transcription by pol II at the GAL1 promoter three- to fivefold above the level of activation by GAL4-VP16 alone. Gel mobility shift assays showed that NHP6A promotes the formation of a complex with TBP and TFIIA at the TATA box that has enhanced affinity for TFIIB.
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PMID:Yeast HMG proteins NHP6A/B potentiate promoter-specific transcriptional activation in vivo and assembly of preinitiation complexes in vitro. 894 17

Human NC2 utilizes a unique mechanism of repression of transcription by associating with TBP and inhibition of preinitiation complex formation. Here we have cloned two genes from Saccharomyces cerevisiae and functionally characterized them as yeast NC2. We show that yeast NC2 binds to TBP as a heterodimer and represses RNA polymerase II transcription during assembly of the preinitiation complex. Yeast NC2 is highly homologous to its human counterpart within histone fold domains. C-Terminal regions previously discussed to be important for repression in man are in part not conserved. The human alpha but not the beta subunit efficiently heterodimerizes and represses transcription in combination with the corresponding yeast subunit. Yeast and human NC2 inhibit transcription in the presence of yeast and human TBP. However, repression is optimal within one species. The N-terminus of human TBP supports repression of transcription by human but not by yeast NC2.
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PMID:Characterization of the basal inhibitor of class II transcription NC2 from Saccharomyces cerevisiae. 894 34

The human RNA polymerase II and III snRNA promoters share a common basal element, the proximal sequence element (PSE), which is recognized by a complex we refer to as the snRNA-activating protein complex (SNAPc). Biochemical purifications suggest that SNAPc is composed of at least four polypeptides of 43, 45, 50 and 190 kDa, as well as variable amounts of the TATA box binding protein, TBP. cDNAs encoding the 43 and 45 kDa subunits, SNAP43 and SNAP45, have been isolated, but there is no evidence that either of these subunits contacts DNA. Here we report the isolation of cDNAs encoding the 50 kDa subunit of SNAPc, SNAP50. The open reading frame predicts a 411 amino acid protein, which contains two potential zinc finger motifs. Depletions with anti-SNAP50 antibodies inhibit RNA polymerase II and III snRNA gene transcription in vitro. SNAP50 interacts with SNAP43 in co-immunoprecipitation experiments, but not with SNAP45 or TBP. UV cross-linking experiments suggest that SNAP50 contacts DNA in the SNAP complex. These results are consistent with the same core SNAP complex recognizing the PSEs of RNA polymerase II and III snRNA promoters, and provide an initial view of the architecture of the SNAP complex.
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PMID:Cloning and characterization of SNAP50, a subunit of the snRNA-activating protein complex SNAPc. 900 88

The products of the yeast CDC73 and PAF1 genes were originally identified as RNA polymerase II-associated proteins. Paf1p is a nuclear protein important for cell growth and transcriptional regulation of a subset of yeast genes. In this study we demonstrate that the product of CDC73 is a nuclear protein that interacts directly with purified RNA polymerase II in vitro. Deletion of CDC73 confers a temperature-sensitive phenotype. Combination of the cdc73 mutation with the more severe paf1 mutation does not result in an enhanced phenotype, indicating that the two proteins may function in the same cellular processes. To determine the relationship between Cdc73p and Paf1p and the recently described holoenzyme form of RNA polymerase II, we created yeast strains containing glutathione S-transferase (GST)-tagged forms of CDC73, PAF1, and TFG2 functionally replacing the chromosomal copies of the genes. Isolation of GST-tagged Cdc73p and Paf1p complexes has revealed a unique form of RNA polymerase II that contains both Cdc73p and Paf1p but lacks the Srbps found in the holoenzyme. The Cdc73p-Paf1p-RNA polymerase II-containing complex also includes Gal11p, and the general initiation factors TFIIB and TFIIF, but lacks TBP, TFIIH, and transcription elongation factor TFIIS as well as the Srbps. The Srbp-containing holoenzyme does not include either Paf1p or Cdc73p, demonstrating that these two forms of RNA polymerase II are distinct. In confirmation of the hypothesis that the two forms coexist in yeast cells, we found that a TFIIF-containing complex isolated via the GST-tagged Tfg2p construct contains both (i) the Srbps and (ii) Cdc73p and Paf1p. The Srbps and Cdc73p-Paf1p therefore appear to define two complexes with partially redundant, essential functions in the yeast cell. Using the technique of differential display, we have identified several genes whose transcripts require Cdc73p and/or Paf1p for normal levels of expression. Our analysis suggests that there are multiple RNA polymerase II-containing complexes involved in the expression of different classes of protein-coding genes.
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PMID:Cdc73p and Paf1p are found in a novel RNA polymerase II-containing complex distinct from the Srbp-containing holoenzyme. 903 43

The multi-protein complex SL1, containing TBP, which is essential for RNA polymerase I catalyzed transcription, has been analyzed in fission yeast. It was immunopurified based on association of component subunits with epitope-tagged TBP. To enable this analysis, a strain of Schizosaccharomyces pombe was created where the only functional TBP coding sequences were those of FLAG-TBP. RNA polymerase I transcription components were fractionated from this strain and the TBP-associated polypeptides were subsequently immunopurified together with the epitope- tagged TBP. An assessment of the activity of this candidate SL1 complex was undertaken cross-species. This fission yeast TBP-containing complex displays two activities in redirecting transcriptional initiation of an S. pombe rDNA gene promoter cross-species in Saccharomyces cerevisiae transcription reactions: it both blocks an incorrect transcriptional start site at +7 and directs initiation at the correct site for S. pombe rRNA synthesis. This complex is essential for accurate initiation of the S.pombe rRNA gene: rRNA synthesis is reconstituted when this S.pombe TBP-containing complex is combined with a S.pombe fraction immunodepleted of TBP.
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PMID:An immunoaffinity purified Schizosaccharomyces pombe TBP-containing complex directs correct initiation of the S.pombe rRNA gene promoter. 909 73


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